Lab

Testosterone (Quaigen FastPack)

Effective Date: 
Mon, 10/04/2021
Policy: 

Principle

The FastPack® IP Testo and FastPack® Testo Immunoassay is a competitive chemiluminescence assay.

 Primary incubation: Antibody solution (a buffer solution containing a monoclonal C3-testosterone-specific antibody labeled with alkaline phosphatase) [100 µL] reacts with testosterone from the patients sample, control, or calibrator [100 µL].

 Secondary incubation: The reaction mixture is added to paramagnetic particle with covalently coupled testosterone. During this incubation, the testosterone-coated beads compete with the sample testosterone.

 Removal of unbound materials: The paramagnetic particles are washed with wash buffer [0.2 mL/wash] to remove unbound materials.

 Substrate addition and detection: Chemiluminogenic substrate [140 µL] is added to the solid-phase bound complex and results in “glow” chemiluminescence, which is measured using the FastPack® IP System and FastPack® System analyzer.

 The amount of bound labeled-antibody is inversely proportional to the concentration of testosterone in the sample.

Supplies and Reagents

Each FastPack® IP carton contains:

 30 FastPack® IP Each FastPack® carton contains:

 50 FastPacks Each FastPack® Contains:

 Paramagnetic Particles, 150 µL Paramagnetic particles with covalently coupled testosterone in buffer containing 0.1% sodium azide as a preservative.

 Testosterone Antibody Solution, 100 µL Antibody solution containing mouse monoclonal antibody labeled with alkaline phosphatase in a protein matrix containing 0.03% Proclin® 150 as a preservative.

 Wash Buffer, 2.0 mL Tris buffer containing surfactants.

 Substrate, 140 µL ImmuGlow™: Indoxyl-3-phosphate and lucigenin in buffer containing preservatives.

Assay/Reagent Handling

STORAGE INSTRUCTIONS Store at 2 – 8 °C.

Specimen Collection/Preparation

1. Serum, EDTA or lithium-heparin plasma samples can be used for the FastPack® IP and FastPack® hCG Immunoassay. 2. The National Committee for Clinical Laboratory Standards (NCCLS) provides the following recommendations for handling, processing and storing blood.7,8 A. Collect all blood samples observing routine precautions for venipuncture. B. For plasma samples:

 Collect samples in an EDTA (lavender top) or heparinized (green top) tube.

 Mix the tube immediately after collection by gently inverting it several times.

 Plasma should be separated from the cells by centrifugation within 3 hours from time of collection and stored at 2–8º C. Transfer the plasma from the original tube for storage.

 If not tested within 24 hours, the sample should be frozen at –20º C or colder.

Do not freeze samples (-20 °C) for more than two months.  Frozen samples should be thawed completely and mixed by gentle inversion prior to use.  Samples should be free of Fibrin, Red Blood Cells, or other particulate material for optimal results. Samples showing turbidity and/or particulate matter should be centrifuged prior to use. Ensure the samples are free of bubbles. Human samples should be handled in accordance with the OSHA standard on Bloodborne Pathogens.

Procedure: 

The FastPack® IP System analyzer is ready to run a FastPack® IP at any time as long as it is turned on, has reached operating temperature and pressure, and has been calibrated. If the analyzer is not at operating temperature, the analyzer will not operate and the BLUE button will not function. Leave the analyzer turned on 24 hours a day so that it will always be at operating temperature. The analyzer performs a comprehensive Self Diagnostic test every midnight to ensure the system is functioning properly. When the Self Diagnostic test is running, the analyzer door will be locked shut.

  1. Verify that the analyzer is in “Ready” mode.
  2. Remove the FastPack® IP from its box. Check to make sure it is the correct test type. Ensure there are no external fluid leaks or any burst chambers on the FastPack® IP.
  3. Label Patient’s Name/ID # and the operator’s initials on the peel-off FastPack® IP label.
  4. Press and hold the pippette plunger down comletely so that the metal grippers are extended and open.
  5. While holding the plunger down, firmly press the pipette into the pipette tip until it snaps in place then release the plunger.
  6. Be sure the pipette tip is seated properly on the end of the pipette.
  7. Gently press the pipette plunger down to the first stop and hold.  Then place the pipette tip into the sample and withdraw sample slowly releasing the plunger.  Inspect for bubbles
  8. With your finger off the pipette plunger, fully insert the filled pipette tip into the FastPack IP injection port.
  9. In one continuous motion, press the pipette plunder all the way down to the second stop.  This will inject the sample into the FastPack.
  10. Place the FastPack IP on the door of the analyzer.  Alight the pins on the door with the holes in the FastPack IP.  Close the analyzer door.
  11. Press the Blue Start Button
  12. Record result

EXPECTED RANGE

Males: >214 ng/dL

Females: <23 ng/dL

Serum samples were obtained from 125 random males and 173 random females ranging in age from 18 to 94 years. Samples were obtained from normal, healthy blood donors without any clinically abnormal indications. Testosterone levels were determined using the FastPack® IP Testo and Fastpack® Testo Immunoassay in conjunction with the FastPack® IP System analyzer in order to establish the testosterone concentration in the normal population. Results are in ng/dL.

Range of linearity:  The measuring range was evaluated following the CLSI EP6-A guideline. For Testosterone in serum, Lithium Heparin plasma, and K2 EDTA plasma as tested by the FastPack Testosterone assay, the measuring range is from 23.0 ng/dL (Limit of Quantitation) to 1600 ng/dL. A recovery study was performed to confirm the measuring range. Study results are summarized in the tables below. Diluting samples above 1,600 ng/dL is not recommended.

Quality Control

2 levels of quality control are run whenever;

Patient testing is performed.*

· A calibration is performed.

· Repair maintenance is performed.

· Improper storage or handling of FastPacks® is suspected.

· Questionable patient results are obtained

  1. Open the FastPack® IP Control Kit. Remove contents.
  2. Write “CX”, depending upon the Control Vial used and lot number, and the operator’s initials on the peel-off FastPack® IP label.
  3. Invert Control Vial 6-8 times before opening. 
  4. Closely follow steps to run test (see above).
  5. When test is complete, analyzer will beep.
  6. The analyzer will provide the test result on the display. The result will remain displayed for one minute after the door is opened or until another test is run. When a new test is run, the previous test result is erased from the analyzer memory and display.
  7. Analyzer will start beeping and display “Insert FastPack® in Printer” until result is printed.
  8. Remove and inspect the FastPack® IP. Check the inside of the Analyzer door for fluid. If there is fluid on the FastPack® IP or Analyzer, disregard the result and properly dispose of the pack. Implement the cleaning procedure. 
  9. Slip the FastPack® IP into the external printer from the left side with the label side up and the label facing towards the rear of the external printer.
  10. Remove the FastPack® IP from the left side of the external printer.
  11. Find the result printed on the FastPack® IP peel-off label. Control Result Units Date of Test Instrument Serial#.
  12. All the necessary information for Quality Control is now included on the peel-off label.
  13. Match each control lot number from the Control Range Card with the lot number on the control vials. If each of these lot numbers match, then verify that the result printed on the FastPack® IP is within range for the appropriate control.
  14. Record QC in Harvest 
  15. Discard the used FastPack® IP into a Biohazard container.

Calibration

  1. Open the FastPack® IP Calibration Kit. Remove contents
  2. Place “Calibration card” on the door. Align the pins on the door with the holes in the FastPack
  3. Press the BLUE button
  4. Open the analyzer door. Remove the calibration card. Store card in Calibration Kit. 
  5. Remove the FastPack® IP from its box. Check to make sure it is the correct test type.
  6. Write “CAL 1 or CAL 2 (or CAL 3 for the Vitamin D assay)” along with the operator’s initials on the peel-off FastPack® IP label
  7. Invert the calibrator vial 6-8 times before opening.
  8. Closely follow Run Test steps (see above).
  9. Open analyzer door. Place FastPack® IP on the door. Align the pins on the door with the holes in the FastPack® IP. 
  10. Close the analyzer door.
  11. Press the BLUE button.
  12. The display will confirm whether calibration passed or failed, and display date and time.
  13. Open the analyzer door
  14. Remove and inspect the FastPack® IP. Check the inside of the analyzer door for fluid. If there is fluid on the FastPack® IP or analyzer, disregard the result and properly dispose of the pack. Implement the Cleaning Procedure.
  15. Slip the FastPack® IP into the external printer from the left side with the label side up and the label facing towards the rear of the external printer. 
  16. Remove the FastPack® IP from the left side of the external printer.
  17. Find the result printed on the FastPack® IP peel-off label. Calibrator Pass/Fail Calibration Lot # Date of Test Instrument Serial#
  18. Peel off the label.
  19. Place the printed Calibration label on a Label Record in the appropriate assay section of your Quality Assurance Log.
  20. Discard the FastPack® IP into a Biohazards container.
  21. Repeat the Calibration Procedure. All calibrations require that TWO (2) calibrations be run with the calibrator.
Key Points: 

LIMITATION OF PROCEDURE

 Samples can be measured within the reportable range of the analytical sensitivity and the upper end of the calibration range, 1600 ng/dL.

 Samples >1600 ng/dL should be run using another method. Dilution of out of range results is not recommended.

 Samples from patients who have received preparations of mouse monoclonal antibodies for diagnosis or therapy may contain human anti-mouse antibodies (HAMA). Such samples may show either falsely elevated or depressed values when tested with assay kits employing mouse monoclonal antibodies.

 Heterophilic antibodies in a sample have the potential to cause interference in immunoassay systems. Infrequently, testosterone levels may appear elevated due to heterophilic antibodies present in the patient’s serum or to nonspecific protein binding. If the testosterone level is inconsistent with clinical evidence, additional testosterone testing is suggested to confirm the result.

 For diagnostic purposes, the Fastpack® IP Testo and FastPack® Testo Immunoassay should always be assessed in conjunction with the patient’s medical history, clinical examination and other findings.

 The FastPack® IP Testo and Fastpack® Testo Immunoassay is not for pediatric use. 

REFERENCES

1 Wilson, JD, George, FW, Griffin, JE: The hormonal control of sexual development. Science, 211: 1278 – 1284, 1981.

2 Imperato-Mcginley, J, Guerrero, T, Peterson, RE: Steroid 5 a-reductase deficiency in man: An inherited form of male pseudohermaphroditism. Science, 186:1213 – 1215, 1974.

3 Approved Standard – procedures for the collection of diagnostic blood specimens by venipuncture. 5th Edition: H3-A5: 23(32) 2003, National Committee for Clinical Laboratory Standards (NCCLS)

4 Approved guideline – procedures for the handling and processing of blood specimens, H18-A2;19(21), 1999. National Committee for Clinical Laboratory Standards (NCCLS).

5 Schroff, RJ, Foon, KA, et.al.: Human anti-mouse immunoglobin responses in patients receiving monoclonal antibody therapy. Cancer Res, 45:879 – 885, 1985

6 US Department of Labor, Occupational Safety and Health Administration, 29CFR Part 1910.1030, Occupational Exposure to Bloodborne Pathogens; Final Rule. Federal Register 1991; 56(235): 64175-82.

7 Gronowski AM, Landau-Levine M. Reproductive Endocrine Function in Tietz Textbook of Clinical Chemistry. Ed. Edward R. Ashwood, and Carl A. Burtis. 3rd ed. N.p.:W. B. Saunders Company, 1999. 1603-1636.

Beta hCG (Qualigen Fastpack)

Effective Date: 
Tue, 10/05/2021
Policy: 

Principle

The FastPack® IP and FastPack® hCG Immunoassay is a chemiluminescence assay based on the “sandwich” principle.

 Primary incubation: A monoclonal anti-hCG antibody labeled with alkaline phosphatase [100 µL] reacts with hCG from the patient’s sample, control or calibrator [25 µL].

 Secondary incubation: A second monoclonal anti-hCG antibody covalently coupled to biotin and pre-bound to streptavidin-coated paramagnetic particles [150 µL] is combined with the reaction mixture.

 Removal of unbound materials: The paramagnetic particles are repeatedly washed with wash buffer [0.2 mL/wash] to remove unbound materials.

 Substrate addition and detection: Chemiluminogenic substrate [140 µL] is added to the solid-phase bound complex and results in “glow” chemiluminescence, which is measured using the FastPack® IP System.

 The amount of bound labeled-antibody is directly proportional to the concentration of hCG in the sample.

Supplies and Reagents

Each FastPack® IP carton contains:

 30 FastPack® IPs Each FastPack® carton contains:

 50 FastPacks Each FastPack® IP or FastPack® Contains:

 Paramagnetic Particles, 150 µL Biotin-mouse monoclonal anti-βhCG antibody bound to streptavidin-coated paramagnetic particles in buffer containing <0.1% sodium azide and 0.1% ProClin® 300 as a preservative.

 hCG Antibody Solution 1, 100 µL Antibody solution containing a mouse monoclonal anti-βhCG antibody labeled with alkaline phosphatase in a protein matrix containing <0.1% sodium azide and 0.1% ProClin® 300 as a preservative.

 Wash Buffer, 2.0 mL Tris buffer containing surfactants.

 Substrate, 140 µL ImmuGlow™ Plus: Indoxyl-3-phosphate and lucigenin in buffer containing preservatives. Materials required but not provided  FastPack® IP System

 FastPack® hCG Calibrator Kit – Cat. No. 25000035

 FastPack® hCG Sample Diluent – Cat. No. 25000036  Quality control materials (see “Quality Control” section) 

Assay/Reagent Handling

STORAGE INSTRUCTIONS Store at 2 – 8 °C.

SPECIMEN COLLECTION/PREPARATION

1. Serum, EDTA or lithium-heparin plasma samples can be used for the FastPack® IP and FastPack® hCG Immunoassay. 2. The National Committee for Clinical Laboratory Standards (NCCLS) provides the following recommendations for handling, processing and storing blood.7,8 A. Collect all blood samples observing routine precautions for venipuncture. B. For plasma samples:

 Collect samples in an EDTA (lavender top) or heparinized (green top) tube.

 Mix the tube immediately after collection by gently inverting it several times.

 Plasma should be separated from the cells by centrifugation within 3 hours from time of collection and stored at 2–8º C. Transfer the plasma from the original tube for storage.

 If not tested within 24 hours, the sample should be frozen at –20º C or colder.

 

Procedure: 

The FastPack® IP System analyzer is ready to run a FastPack® IP at any time as long as it is turned on, has reached operating temperature and pressure, and has been calibrated. If the analyzer is not at operating temperature, the analyzer will not operate and the BLUE button will not function. Leave the analyzer turned on 24 hours a day so that it will always be at operating temperature. The analyzer performs a comprehensive Self Diagnostic test every midnight to ensure the system is functioning properly. When the Self Diagnostic test is running, the analyzer door will be locked shut.

  1. Verify that the analyzer is in “Ready” mode.
  2. Remove the FastPack® IP from its box. Check to make sure it is the correct test type. Ensure there are no external fluid leaks or any burst chambers on the FastPack® IP.
  3. Label Patient’s Name/ID # and the operator’s initials on the peel-off FastPack® IP label.
  4. Press and hold the pippette plunger down comletely so that the metal grippers are extended and open.
  5. While holding the plunger down, firmly press the pipette into the pipette tip until it snaps in place then release the plunger.
  6. Be sure the pipette tip is seated properly on the end of the pipette.
  7. Gently press the pipette plunger down to the first stop and hold.  Then place the pipette tip into the sample and withdraw sample slowly releasing the plunger.  Inspect for bubbles
  8. With your finger off the pipette plunger, fully insert the filled pipette tip into the FastPack IP injection port.
  9. In one continuous motion, press the pipette plunder all the way down to the second stop.  This will inject the sample into the FastPack.
  10. Place the FastPack IP on the door of the analyzer.  Alight the pins on the door with the holes in the FastPack IP.  Close the analyzer door.
  11. Press the Blue Start Button
  12. Record result

Sample Dilution

  1. Using a NEW pipette tip, draw a fresh 25 µL patient sample
  2. Add this sample to a Sample Diluent tube.
  3. Replace the cap and gently mix by inverting the tube back and forth several times. 
  4. Using a NEW pipette tip, draw a 25 µL sample from the mixture in the Sample Diluent tube.
  5. Place this sample into a fresh FastPack® IP.
  6. Press RED button several times to scroll through the menu till you see “Set Dilution ON” 
  7. Press the BLUE button to accept.

EXPECTED VALUES/REFERENCE INTERVALS

<1.8 – 3.0 mIU/mL for non-pregnant females.

Samples were obtained from 241 individuals, 115 males and 126 non-pregnant females. Samples were obtained from apparently healthy blood donors without any clinically abnormal indications. hCG levels were determined using the FastPack® IP and FastPack® hCG Immunoassay in conjunction with the FastPack® IP System in order to establish the hCG concentrations in the reference populations. The reference interval (5th to 95th percentiles) for the FastPack® IP and FastPack® hCG Immunoassay for males is <1.8 mIU/mL and <1.8 – 3.0 mIU/mL for non-pregnant females. These reference intervals reflect the donor population of this study group. 

Range of linearity For hCG as tested by the FastPack® IP and FastPack® hCG assay, based on the CLSI EP-6A evaluation the method has been demonstrated to be linear from 1.8 mIU/mL to 940.6 mIU/mL within 5 mIU/mL in the interval between 1.8 and 50 mIU/mL and 25 mIU/mL in the interval between 50 and 1000 mIU/mL hCG. FastPack® IP and FastPack® hCG Immunoassay E-5 P/N 64000023 Rev. 004 (04/17) Linearity Upon Dilution Two serum pools with high endogenous concentrations of hCG were diluted 1:2, 1:4, 1:8, and 1:16 with a protein- based Tris buffer diluent and quantified in triplicate determinations with one lot of FastPack® IP and FastPack® hCG reagents on a single FastPack® IP instrument. Measured values of the dilutions were compared to their expected values (determined in the same assay) based on the measured value of the Neat sample and the respective dilution factors. (% Recovery = [Observed value/Expected Value] X 100). 

Quality Control

2 levels of quality control are run whenever;

Patient testing is performed.*

 A calibration is performed.

 Repair maintenance is performed.

 Improper storage or handling of FastPacks® is suspected.

 Questionable patient results are obtained

  1. Open the FastPack® IP Control Kit. Remove contents.
  2. Write “CX”, depending upon the Control Vial used and lot number, and the operator’s initials on the peel-off FastPack® IP label.
  3. Invert Control Vial 6-8 times before opening. 
  4. Closely follow steps to run test (see above).
  5. When test is complete, analyzer will beep.
  6. The analyzer will provide the test result on the display. The result will remain displayed for one minute after the door is opened or until another test is run. When a new test is run, the previous test result is erased from the analyzer memory and display.
  7. Analyzer will start beeping and display “Insert FastPack® in Printer” until result is printed.
  8. Remove and inspect the FastPack® IP. Check the inside of the Analyzer door for fluid. If there is fluid on the FastPack® IP or Analyzer, disregard the result and properly dispose of the pack. Implement the cleaning procedure. 
  9. Slip the FastPack® IP into the external printer from the left side with the label side up and the label facing towards the rear of the external printer.
  10. Remove the FastPack® IP from the left side of the external printer.
  11. Find the result printed on the FastPack® IP peel-off label. Control Result Units Date of Test Instrument Serial#.
  12. All the necessary information for Quality Control is now included on the peel-off label.
  13. Match each control lot number from the Control Range Card with the lot number on the control vials. If each of these lot numbers match, then verify that the result printed on the FastPack® IP is within range for the appropriate control.
  14. Record QC in Harvest 
  15.  Discard the used FastPack® IP into a Biohazard container.

Calibration

  1. Open the FastPack® IP Calibration Kit. Remove contents
  2. Place “Calibration card” on the door. Align the pins on the door with the holes in the FastPack
  3. Press the BLUE button
  4. Open the analyzer door. Remove the calibration card. Store card in Calibration Kit. 
  5. Remove the FastPack® IP from its box. Check to make sure it is the correct test type.
  6. Write “CAL 1 or CAL 2 (or CAL 3 for the Vitamin D assay)” along with the operator’s initials on the peel-off FastPack® IP label
  7. Invert the calibrator vial 6-8 times before opening.
  8. Closely follow Run Test steps (see above).
  9. Open analyzer door. Place FastPack® IP on the door. Align the pins on the door with the holes in the FastPack® IP. 
  10. Close the analyzer door.
  11. Press the BLUE button.
  12. The display will confirm whether calibration passed or failed, and display date and time.
  13. Open the analyzer door
  14. Remove and inspect the FastPack® IP. Check the inside of the analyzer door for fluid. If there is fluid on the FastPack® IP or analyzer, disregard the result and properly dispose of the pack. Implement the Cleaning Procedure.
  15. Slip the FastPack® IP into the external printer from the left side with the label side up and the label facing towards the rear of the external printer. 
  16. Remove the FastPack® IP from the left side of the external printer.
  17. Find the result printed on the FastPack® IP peel-off label. Calibrator Pass/Fail Calibration Lot # Date of Test Instrument Serial#
  18. Peel off the label.
  19. Place the printed Calibration label on a Label Record in the appropriate assay section of your Quality Assurance Log.
  20. Discard the FastPack® IP into a Biohazards container.
  21. Repeat the Calibration Procedure. All calibrations require that TWO (2) calibrations be run with the calibrator.
Key Points: 

LIMITATIONS OF PROCEDURE

 Plasma samples to be collected using EDTA or lithium-heparin as the anticoagulants.  Specimens can be detected within the reportable range of the limit of detection (1.8 mIU/mL hCG) and the upper end of the calibration range, 1000 mIU/mL and reliably measured at concentrations at and above the LOQ (3.1 mIU/mL). Values below the LOD should be reported as “<1.8 mIU/mL hCG” and values above the range should be reported as “>1000 mIU/mL hCG” if not diluted and re-tested.  Samples >1000 mIU/mL should be reported as such or re-run using another method. Samples may be diluted using the hCG sample diluent until within range of the assay.  FastPack® IP and FastPack® hCG Immunoassay does not show a high-dose hook effect up to 500,000 mIU/mL.  Specimen from patients who have received preparations of mouse monoclonal antibodies for diagnosis or therapy may contain human anti-mouse antibodies (HAMA). Such specimens may show either falsely elevated or depressed values when tested with assay kits employing mouse monoclonal antibodies.  Heterophilic antibodies in a sample have the potential to cause interference in immunoassay systems. Infrequently, hCG levels may appear depressed due to heterophilic antibodies present in the patient’s sample or to nonspecific protein binding. If the hCG level is inconsistent with clinical evidence, additional hCG testing is suggested to confirm the result.  For diagnostic purposes, the FastPack® IP and FastPack® hCG Immunoassay should always be assessed in conjunction with the patient’s medical history, clinical examination and other findings.  The hCG assay has not been evaluated in Point of Care settings.  The concentration of Human Chorionic Gonadotropin (hCG) in a given specimen determined with assays from different manufacturers can vary due to differences in assay methods and reagent specificity. The results reported by the laboratory to the physician must include the identity of the hCG assay method used. Values obtained with different assay methods should not be used interchangeably.

REFERENCES

1 Kardana A, et al. The heterogeneity of hCG. Endocrinology 1991; 129: 1541-1567.

2 Vaitukaitis JL. Recent progress in hormone research 1976; 32: 289.

3 Sokolove PJ, Faix JD. Agreement of intact and beta chain-specific HCG assays in abnormal pregnancy. Journal of Clinical Immunoassay, Fall, 1991; 14, No. 3: 196-199.

4 Vaitukaitis JL, Braunstein GD, Ross GT. A radioimmunoassay which specifically measures human chorionic gonadotropin in the presence of human luteinizing hormone. American Journal of Obstetrics and Gynecology 1972; 113: 751-758.

5 Norman RJ, Buck RH, Joubert SM. Comparison of human chorionic gonadotrophin concentrations in the sera of patients with normal and abnormal pregnancy measured by radioimmunoassay and immunoradiometric assay. South African Medical Journal April, 1989; 75: 318-319.

6 Schroff, RJ, Foon, KA, et.al: Human anti-mouse immunoglobin responses in patients receiving monoclonal antibody therapy. Cancer Res, 45:879 – 885, 1985 7 Approved Standard – procedures for the collection of diagnostic blood specimens by venipuncture. 5th Edition: H3-A5: 23(32), 2003, National Committee for Clinical Laboratory Standards (NCCLS) 8 Approved guideline – procedures for the handling and processing of blood specimens, H18-A2; 19(21), 1999. National Committee for Clinical Laboratory Standards (NCCLS)

Strep A Molecular (Cepheid GeneXpert)

Effective Date: 
Mon, 10/04/2021
Policy: 

Principle

The test is performed on the Cepheid GeneXpert Instrument Systems. With this platform, the operator can run the test by performing three simple steps: 1) transfer liquid sample to the cartridge with a transfer pipette, 2) run the test on the GeneXpert instrument, and 3) read the results. The GeneXpert automates and integrates sample preparation, nucleic acid extraction, amplification, and detection of the target sequences in clinical specimens by using real-time PCR. The system consists of a GeneXpert instrument, computer, and disposable fluidic cartridges that are designed to complete sample preparation and realtime PCR. The system requires the use of single-use disposable GeneXpert cartridges that hold the PCR reagents and host the PCR processes. Because the cartridges are self-contained, the risk of cross-contamination between samples is minimized. The Xpert Xpress Strep A test includes reagents for the detection of Group A streptococcal bacterial DNA from throat swab specimens obtained from patients with signs and symptoms of pharyngitis. A Sample Processing Control (SPC) and a Probe Check Control (PCC) are also included in the cartridge. The SPC is present to control for an adequate amplification process and to monitor for the presence of inhibitors in the PCR reaction. The PCC verifies reagent rehydration, PCR tube filling, and all reaction components, including probes and dyes, are present and functional in the cartridge. An Early Assay Termination function provides positive results if the signal from the target DNA reaches a predetermined threshold before the full 43 PCR cycles have been completed. When the Strep A target level is high enough to generate very early Cts (≤ 30 Cts), the SPC amplification curve will be not seen and its results will not be reported as the SPC Ct may not reach the expected cycle threshold in high Strep A titer specimens.

Supplies and Reagents

Xpert Xpress Strep A cartridges

Storage and Handling • Store the Xpert Xpress Strep A cartridges at 2–28 °C until the expiration date provided on the label. • Do not open the cartridge lid until you are ready to perform testing. • Do not use cartridges that have passed the expiration date. • Do not use a cartridge that is wet or has leaked.

Materials Required but Not Provided

Copan Liquid Amies Elution Swab (ESwab™) Collection and Transport System. Any of the following ESwab collection kits may be used: • Copan 480C with 50 kits per shelf pack, white capture cap collection kit • Copan 480CE with 50 kits per shelf pack, pink capture cap collection kit • Copan catalog number 480CFA with 50 kits per shelf pack; purple non-capture cap collection kit.

Assay/Reagent Handling

Do not open the Xpert Xpress Strep A cartridge lid except when adding specimen. • Do not use a cartridge that has been dropped after removing it from the packaging. • Do not shake the cartridge. Shaking or dropping the cartridge after opening the cartridge lid may yield invalid results. • Do not place the sample ID label on the cartridge lid or on the barcode label of the cartridge. • Do not use a cartridge with a damaged barcode label. • Do not use a cartridge that has a damaged reaction tube. • It is recommended that the Xpert Xpress Strep A cartridges be at room temperature (20 – 30°C) when used for testing. • Each single-use Xpert Xpress Strep A cartridge is used to process one test. Do not reuse processed cartridges. • Each single-use disposable pipette is used to transfer one specimen. Do not reuse disposable pipettes. • Do not use a cartridge if it appears wet or if the lid seal appears to have been broken. • Wear clean lab coats and gloves. Change gloves between the handling of each specimen.

Procedure: 

Important Start the test within 30 minutes of adding the sample to the cartridge.

Preparing the Cartridge

To add the specimen to the GeneXpert cartridge:

1. Obtain the following items: Xpert Xpress Strep A cartridge, 300 µL transfer pipette (provided), and an appropriately collected and labeled test sample.

2. Inspect the test cartridge for damage. If damaged, do not use it.

3. Mix the patient specimen by vigorously shaking the specimen transport tube for 5 seconds. 4. Open the cartridge by lifting the cartridge lid.

5. Unscrew the specimen transport tube cap (do not remove the cap). Remove the transfer pipette from the wrapper by opening the end next to the bulb. 

6. Open the cap on the specimen transport tube. Squeeze the bulb of the transfer pipette completely and place the pipette tip in the ESwab transport medium tube containing the patient specimen.

7. Release the bulb to fill the pipette with the patient specimen.

8. To transfer the patient specimen to the cartridge, squeeze the bulb of the transfer pipette completely again to empty the contents of the pipette into the large opening (Sample Chamber) in the cartridge.

     Note Take care to dispense the entire volume of liquid into the Sample Chamber. False negative or INVALID results           may occur if insufficient sample is added to the cartridge. 

9. Close the cartridge lid.

10. Dispose of the used pipette in an appropriate waste container.

Run Test

1. Turn on the GeneXpert Instrument System

2. Log on to the System software. The login screen appears. Type your user name and password.

3. In the GeneXpert System window, click Create Test (GeneXpert Dx) or Orders followed by Order Test (Infinity).

4. Scan or type in the Patient ID (optional). If typing the Patient ID, make sure the Patient ID is typed correctly. The Patient ID is shown on the left side of the View Results window and is associated with the test result.

5. Scan or type in the Sample ID. If typing the Sample ID, make sure the Sample ID is typed correctly. The Sample ID is shown on the left side of the View Results window and is associated with the test result.

6. Scan the barcode on the Xpert Xpress Strep A cartridge. Using the barcode information, the software automatically fills the boxes for the following fields: Reagent Lot ID, Cartridge SN, Expiration Date, and Selected Assay.

     Note If the barcode on the Xpert Xpress Strep A cartridge does not scan, then repeat the test with a new cartridge.

7. Click Start Test (GeneXpert Dx) or Submit (Infinity) if Auto-Submit is not enabled. In the dialog box that appears, type your password, if required. For the GeneXpert Dx Instrument:

A. Locate the module with the blinking green light, open the instrument module door and load the cartridge.

B. Close the door. The test starts and the green light stops blinking. When the test is finished, the light turns off and the door will unlock. Remove the cartridge.

C. Dispose of used cartridges in the appropriate sample waste containers according to your institution's standard practices. 

Viewing and Printing Results

This section lists the basic steps for viewing and printing results. For more detailed instructions on how to view and print the results, see the GeneXpert Dx System Operator Manual or the GeneXpert Infinity System Operator Manual.

1. Click the View Results icon to view results.

2. Upon completion of the test, click the Report button of the View Results window to view and/or generate a PDF report file.

Interpretation of Results

The results are interpreted automatically by the GeneXpert Instrument Systems and are shown in the View Results window. The possible results and interpretations are shown in Table 2.

Table 2. Xpert Xpress Strep A Results and Interpretations Result Interpretation

Strep A NOT DETECTED  Strep A target DNA is not detected. • SPC: PASS; SPC has a Ct within the valid range and endpoint above the threshold setting. • PCC: PASS; all probe check results pass.

Strep A DETECTED Strep A target DNA is detected. • Strep A: Ct is within the valid range. • SPC: NA (not applicable); SPC signal is not part of the result interpretation algorithm if Strep A is detected since SPC signal may be suppressed due to competition with Strep A. • PCC: PASS; all probe check results pass.

Strep A: INVALID • SPC: does not meet acceptance criteria. • PCC: PASS; all probe check results pass. Repeat test according to the instructions in Section 17.2, Retest Procedure below.

ERROR • Presence or absence of Strep target DNA cannot be determined. • Strep A: NO RESULT • SPC: NO RESULT • PCC: FAIL*; all or one of the probe check results fail. * If the probe check passed or shows NA, the error is caused by the maximum pressure limit exceeding the acceptable range or by a system component failure. Repeat test according to the instructions in Section 17.2, Retest Procedure below.

NO RESULT • See Figure 8. Presence or absence of Strep A target DNA cannot be determined. A NO RESULT indicates that insufficient data were collected. For example, cartridge integrity test failed, the operator stopped a test that was in progress or a power failure occurred. • Strep A: NO RESULT • SPC: NO RESULT • PCC: NA (not applicable)* * If the probe check shows NA, the error caused by the maximum pressure limit exceeding the acceptable range terminates the run prior to probe check. Repeat test according to the instructions in Section 17.2, Retest Procedure below.

Retest Procedure

To retest an INVALID, NO RESULT, or ERROR result (indeterminate result), use a new cartridge. Use the leftover sample from the original ESwab transport medium tube.

1. Mix the leftover patient specimen by vigorously shaking the specimen transport tube for 5 seconds.

2. Open the cartridge by lifting the cartridge lid.

3. Unscrew the specimen transport tube cap (do not remove the cap). Remove the transfer pipette from the wrapper by opening the end next to the bulb.

4. Lift the cap with the attached swab from the transport tube (do not remove the swab completely from the transport tube). Squeeze the bulb of the transfer pipette completely and place the pipette tip in the ESwab transport medium tube containing the patient specimen.

5. Release the bulb of the pipette to fill the pipette with the patient specimen. 6. To transfer the patient specimen to the cartridge, squeeze the bulb of the transfer pipette completely again to empty the contents of the pipette into the large opening (Sample Chamber). Close the cartridge lid.

8. Dispose of the used pipette in an appropriate waste container. 

Reference Range/Expected Values

Not Detected

Expected Values In multi-center clinical studies for the Xpert Xpress Strep A , 577 throat swab specimens were analyzed. Of the 577 specimens, 326 (56.5%) were collected from female subjects and 251 (43.5%) from male subjects.

Quality Control

Summary. Each Xpert cartridge produces a valid (positive or negative) test result, an ERROR result, or an INVALID result, depending on performance characteristics of the above internal controls that are run on every cartridge.

Cepheid’s GeneXpert System is a closed platform that employs single-use, self-contained Xpert cartridges. Each Xpert cartridge contains all necessary reagents for the detection of target nucleic acids using the polymerase chain reaction (PCR). As each individual test is performed, the Instrument Status, Sample Processing, Integrity of PCR Reagents, and PCR Efficiency are evaluated. These internal quality control features verify multiple aspects of assay performance for every sample tested.

1. Instrument System Control (Check Status): Once an Xpert cartridge has been loaded into a GeneXpert module and before the sample processing steps begin, the software checks the optics, the readiness of the module’s mechanical components, the ambient temperature of the module to assure proper performance of PCR, and the physical integrity of the cartridge. • If Check Status fails for any reason, the assay is terminated and an ERROR is reported

2. Reagent Control (Probe Check): Probe Check is performed on every cartridge after onboard sample preparation, reagent mixing, probe integrity, and reaction tube filling, but before initiation of PCR. During Probe Check, fluorescence readings are measured in the reaction tube for each probe and compared to default settings established by Cepheid. • If the readings match the default settings, the Probe Check control passes • If the readings do not match the default settings, the assay is terminated and an ERROR is reported

3. Sample Processing Control (SPC)/Cepheid Internal Control (CIC): The SPC and CIC are exogenous (non-sample, non-analyte) nucleic acid pre-loaded in the cartridge that coextracts and co-amplifies along with the sample nucleic acids. The SPC and/or CIC verifies the (i) effectiveness of on board sample processing, (ii) integrity of extracted nucleic acids, (iii) favorable reaction conditions for PCR performance, and (iv) absence of excess PCR inhibitors. • If the SPC or CIC Ct is not within the valid range and the endpoint is below the minimum setting in an analyte-negative test, an INVALID result is reported Genotyping assays do not include an SPC because the presence of at least one target allele indicates that sample processing and PCR reaction conditions were favorable. • If no target allele is detected in a genotyping assay, an INVALID result is reported

4. Internal Quantitative Standard High and Low (IQS-H and IQS-L): IQS-H and IQS-L are two Armored RNA® constructs in the form of a dry bead that goes through the whole assay process. They are used for quantification by using lot specific parameters for the calculation of assay specific RNA concentration in the sample. Additionally IQS-H and IQS-L detect specimen associated inhibition of the RT-PCR reaction.

5. Sample Volume Adequacy (SVA): Ensures the sample was correctly added to the cartridge. The SVA verifies that the correct in-volume of sample has been added in the sample chamber. The SVA verifies the sample addition. • If there is no sample or not enough sample added, an ERROR will be displayed.

6. Sample Adequacy Control (SAC): The SAC is employed in assays that require that the sample contains sufficient patient cells for reliable assay performance. The SAC reagents amplify and detect an endogenous single-copy human gene in the patient sample. The SAC coextracts and co-amplifies with the other nucleic acids in the sample. • If the SAC is not within the valid range and the endpoint is below the minimum setting in an analyte-negative test, an INVALID result is reported

7. Other Control Features (all assays): Cepheid’s Xpert assay software employs proprietary relational algorithms for each amplified analyte. These can include minimum and maximum PCR cycle cutoffs, baseline correction, and additional processes to reduce the effects of unusual curves or target relationships in multiple-target assays. • If the criteria of these algorithms are not met, an ERROR or INVALID result is reported

External Controls: not available in the kit, but they can be used (positive and negative controls).

Calibration

1. Place the Xpert Calibration Software CD 1 in the computer connected to the GeneXpert Dx instrument, or in the kiosk computer for the Infinity.

2. On the computer desktop, right-click the Computer icon and a drop-down menu will appear. Click Open, then right-click on the applicable drive letter for your CD drive. Select Open from the drop-down menu, and the files located on the CD will then be displayed. Find and right-click the XpertCalibration.exe application, and when the drop-down menu appears, click Open to launch the software. Note: The software may take some time to load from the CD.

3. The Terms of Service screen appears. Use the scroll bar to read through the entire document. You will be asked click the check box (below the screen) to verify that you have read and agree to the Terms of Service before continuing.

4. After agreeing to the Terms of Service, the Login screen will appear. Log in with your GeneXpert Dx or Infinity designated USER NAME and PASSWORD (previously assigned to you by your system administrator). After entering your login information, click the forward arrow button at the bottom of the screen to advance to the next screen (the Xpert Home screen). Note: The user name and password are the same ones you used for the GeneXpert Dx or Xpertise software.  

5. If a login error occurs, recheck the USER NAME and PASSWORD entries for errors. If necessary, reenter the information and retry. After entering your login information, click the forward arrow button at the bottom of the screen to advance to the next screen (the Xpert Home screen).

6. Obtain a sufficient number of cartridges for the number of module to be tested. Important: Do not open cartridge packages until you are ready to scan the cartridge barcodes (in step 15). Note: Only an Administrator can exclude (deselect) individual modules from this calibration test. When determining the number of cartridges that will be needed for this test, the user should be aware of the number of modules that they will be calibrating

Click the Collect Calibration Data icon on the Home screen (See Figure 4). After a few seconds, the first Contact Information screen will appear.

8. When the first of two Contact Information screens appear fill out the fields in the two screens. Use the large navigation arrows at the bottom of the screens to move between the two screens. Note that fields marked with “*“are mandatory fields

Note: The ASP-provided ID code for the Service Provider on the Contact Information screen consists of four characters. (As examples for the United States, use US, followed by two digits, such as US01, US28, etc.).

9. When all information has been entered, click the forward arrow button at the bottom of page 2 of the Contact Information screen. The Open Module Doors screen will appear. See Figure 7. Manually open all module doors to enable cartridge loading.

10. After opening all the module doors, click the forward arrow button at the bottom of the screen. The Module Preparation screen will appear briefly, showing the message, “Please, wait. Modules are being prepared.” Important: Note that the Module Preparation screen may appear only briefly, with its length of visibility determined by the number of modules being calibrated. The next screen you see will be the Select Modules screen.

11. Follow the on-screen software instructions. By default, all detected modules will be marked as selected for calibration. Note: A Basic User cannot deselect modules to exclude them from this calibration test. Only an Admin can click on individual modules to exclude them from calibration, if required. For excluded modules (not selected for calibration), the door position (open or closed) does not matter. Two screens are displayed. The screen on the left shows the screen an Administrator would see in which individual modules can be deselected from calibration. The screen on the right shows the screen a Basic User would see where no deselection can be done. To move to the next screen, click the arrow at the bottom of the screen.

Important: GX-XVI and Infinity systems only: When selecting modules on screen, note which module lights are blinking on the system as you select each bank.

12. After selecting the modules, click the arrow button at the bottom of the screen. If you are logged on as an Administrator, the Confirm module selection screen appears. If you are logged on as a Basic User, this screen will not appear (Skip to step 13).

13. If all modules have been excluded in the above step by mistake, a screen will appear, advising you to start over by returning to the Home screen or exiting the program

14. After confirming your module selection, you will advance to the Scan cartridge screen, where you will be prompted to scan the barcode on the Xpert Calibration cartridge.

Note: Verify you have enough cartridges on hand to perform the calibration procedure for the desired number of modules.

15. Remove the test kit cartridge from the package for the module you’ve previously selected, opening only one cartridge at a time.

16. Scan the cartridge barcode. Do not substitute a cartridge with another after it’s been scanned. Note: If the barcode cannot be scanned, skip the cartridge and contact your ASP for a replacement cartridge, if necessary. If the barcode scanner is damaged, missing or incorrectly configured, contact your ASP for guidance.

a. After scanning the barcode of the cartridge, ensure you open (vent) the cartridge lid and then close it for each cartridge as directed by the software in step b through step e below. Important: Do Not add a sample or reagent to the cartridge. Use ONLY the cartridges in the calibration kit provided. Note: After a cartridge barcode is scanned a green light will blink on the system above the module door where the cartridge will be loaded. Note: If, for some reason, you want to skip the cartridge just scanned, click the SKIP button at the bottom of the screen. An overlay will appear asking for confirmation on skipping the cartridge. To SKIP the cartridge, click the forward arrow at the bottom of the screen. To proceed without skipping the cartridge, click the “X” icon at the left bottom corner of the screen. You are urged to rescan a cartridge (or substitute a new cartridge if necessary) to ensure a module is not skipped.

b. Venting the cartridge for two seconds is sufficient. This screen is animated, showing the cartridge lid being opened and closed. After venting, click the forward arrow at the bottom of the screen to continue.

c. Close the cartridge lid and ensure the module door is fully opened to receive the cartridge.

d. Load the cartridge into the module (with the cartridge reaction tube facing away from you), as directed by the software screens.

Note: Be sure to load scanned cartridges in sequence in the next available module. This will avoid loading cartridges in the wrong location or leaving modules empty

e. If you are calibrating additional modules, continue by scanning the next cartridge. Place each individual scanned cartridge into the next selected open module, pressing the module door securely closed until it latches. As each module door is closed and latched, data collection will automatically start on that specific module. The blinking green light above the module will then become steady green, indicating that calibration testing has started. Important: If a module door is not closed completely (until it latches) after loading a cartridge, the screen will continue to display a message to insert a cartridge, and the calibration test will not run. If you are unable to close and latch a module door after several tries, press the skip button at the bottom of the screen to skip the module with the faulty door and move ahead. Notify your ASP so the module can be serviced.

17. Calibration will take approximately 20 minutes to complete after the final module has been loaded for testing. When the calibration test begins, the Data collection in progress screen appears.

Important: If necessary, a retest of a previously run module may be started without waiting for the present module to complete its test, as described in steps 18b through 18d.

18. After test completion, the module door will open and the light above the module will turn off. Press the right arrow to continue. When the test is complete, click the forward button at the bottom of the screen to begin uploading calibration test results to the Xpert Connectivity Center.

For all users: If the test was unsuccessful, the screen shown in Figure 19 will appear, showing module status. A test retry must be performed. Click the Retry icon in the lower left-hand corner of the screen.

If the arrow at the bottom of the screen is pressed when there is an unsuccessful module test displayed the Confirm continue screen will appear.

You have the option of continuing by pressing the right arrow on the Confirm continue Screen overlay. Choosing this option will result in the flagged module not being retested, and you will begin uploading calibration data as described in step 19. Another option is to return to the Press retry or continue Screen to Retry (retest) the flagged module by clicking on the red “X” icon at the bottom left of the Confirm continue screen. The Retry procedure is described in step d which follows.

d. If the Retry icon appears, click the Retry icon and you will return to the Scan Barcode screen to complete the retest on the affected module(s). Note that the retest can be of two possible types:

I Retry with the same cartridge: For example, a message may appear telling you to vent the cartridge, rescan it, and put it back in the module.

II Retry with a new cartridge: If the cartridge was defective, or had already been used, you will be asked to replace it by scanning the barcode on a new cartridge, venting it, and loading it into the module.

Note: During the course of running retests, modules may need to be skipped if the user runs out of Xpert Calibration cartridges. Please contact your ASP for additional Xpert Calibration cartridges. Rerun Xpert Calibration on any modules that were skipped. At the completion of the Xpert Calibration data collection process modules determined to require service will be flagged as locked to further use. Please contact your local ASP for further assistance in replacing modules requiring service.

19. After successful test completion and calibration data collection, click the forward arrow.   if you have an active internet connection. However, if you have never been internet connected, or have lost your functioning internet connection sometime during the calibration test, a Download activation code error screen will appear instead, instructing you to write calibration data to data CD2 to send to your ASP. In this case, continue to step d (under step 25) of this procedure to continue as a user without an internet connection.

Note: With a functioning internet connection, the system should proceed normally (with step 20), and the activation certificate should begin downloading.

20. When the calibration data has finished uploading, a Quality Assurance check will be performed on the data. If the check is acceptable, the activation code certificate will automatically download. If the test is not acceptable, the affected module(s) will require service and will be locked to further use. Please contact Cepheid or your local ASP for further assistance.

21. After the Activation Code Certificate has downloaded, the Activation Code will be applied to each successfully tested module, and those modules will then be identified with a “+” symbol

22. After all the activation codes have been applied to the successfully-tested modules (those green modules which appear with the plus symbols applied), the Activation complete screen will appear. This screen shows the location of the Calibration Data report, which is available for review, if desired.

23. Remove and discard all calibration cartridges. Do not save partial kits (all unused cartridges must be discarded). When complete, click the Exit icon at the bottom of the screen to exit the program.

24. Note that in certain situations, a screen may appear, asking for exit confirmation.

 

 

Key Points: 

Limitations

Additional follow-up testing by culture is required if the Xpert Xpress Strep A test result is negative and clinical symptoms persist, or there is an outbreak of acute rheumatic fever (ARF). • The performance of the Xpert Xpress Strep A test was evaluated using the procedures provided in this package insert only. Modifications to these procedures may alter the performance of the test. • Careful compliance with the instructions in this package insert and in the Copan Liquid Amies Elution Swab (ESwab) Collection and Transport System package insert is necessary to avoid erroneous results. • The Xpert Xpress Strep A test has been validated only with Copan Liquid Amies Elution Swab (ESwab) Collection Kit (Copan 480C or Copan 480CE or Copan 480CFA). • Because the detection of Streptococcus pyogenes is dependent on the organism’s DNA present in the sample, reliable results are dependent on proper sample collection, handling, and storage. • The Xpert Xpress Strep A test provides qualitative results and does not provide the quantitative value of the organism detected in the specimen. • Mutations or nucleotide polymorphisms in primer or probe binding regions may affect detection of new or unknown Streptococcus pyogenes strains resulting in a false negative result. • A negative test result does not exclude the possibility of infection because the test result may be affected by improper specimen collection, technical error, sample mix-up, or because the number of organisms in the sample is below the limit of detection of the test.

Methodology

Real time Polymerase Chain reaction (PCR) performed on the Cepheid GeneXpert platform

Maintenance

Daily Maintenance: ‒ Discard used cartridges ‒ Put the dust cover when the system is not in use to limitate dust.

• Weekly Maintenance: - Clean the cartridge bay interior ‒ Restart the system (GeneXpert and Computer)

• Monthly Maintenance: ‒ Clean the syringe plunger rod ‒ Clean the instrument surfaces ‒ Clean the fan filters with soapy water (only for GX with white cover) ‒ Archive the results and save it on external support

Clean surfaces;  

Chlamydia Trachomatis/Neisseria Gonorrhoeae (Cepheid GeneXpert)

Effective Date: 
Mon, 10/04/2021
Policy: 

Principle

The Xpert CT/NG test is an automated in vitro diagnostic test for qualitative detection and differentiation of DNA from CT and NG. The test is performed on the Cepheid GeneXpert Instrument Systems. The GeneXpert Instrument Systems automate and integrate sample purification, nucleic acid amplification, and detection of the target sequences in simple or complex samples using real-time PCR and RT-PCR assays. The systems consist of an instrument, personal computer, and preloaded software for running tests on collected samples and viewing the results. The systems require the use of single-use disposable cartridges that hold the PCR reagents and host the PCR process. Because the cartridges are self-contained, cross-contamination between cartridges during the testing process is minimized. For a full description of the systems, refer to the appropriate GeneXpert Instrument System Operator Manual. The Xpert CT/NG test includes reagents for the 5’ exonuclease real-time PCR detection of CT and NG. Reagents for the detection of a Sample Processing Control (SPC), a Sample Adequacy Control (SAC), and a Probe Check Control (PCC) are also included in the cartridge. The SPC is present to control for adequate processing of the target bacteria and to monitor the presence of inhibitors in the PCR reaction.

For Information Only - Not A Controlled Copy Xpert® CT/NG 2 Xpert® CT/NG 301-0234, Rev. K August 2019 The SAC reagents detect the presence of a single copy human gene and monitor whether the sample contains human DNA. The PCC verifies reagent rehydration, PCR tube filling in the cartridge, probe integrity, and dye stability. The primers and probes in the Xpert CT/NG test detect chromosomal sequences in the bacteria. One target is detected for CT (CT1) and two different targets are detected for NG (NG2 and NG4). Both NG targets need to be positive for the Xpert CT/NG test to return a positive NG result. The Xpert CT/NG test is designed for use with the following specimens collected from symptomatic and asymptomatic individuals: female and male urine, patient-collected vaginal swabs (collected in a clinical setting), clinician-collected endocervical swabs, and female and male pharyngeal and rectal swabs. The urine and swab transport reagents are designed to preserve patient specimens to allow transport to the laboratory prior to analysis with the Xpert CT/NG test and are included in the following specimen collection kits: Xpert CT/NG Urine Specimen Collection Kit, the Xpert Urine Specimen Collection Kit, the Xpert CT/NG Vaginal/Endocervical Specimen Collection Kit, the Xpert Vaginal/Endocervical Specimen Collection Kit, and the Xpert Swab Specimen Collection Kit. The specimen is briefly mixed by inverting the collection tube several times and/or aspirating with a transfer pipette. Using the supplied transfer pipette, the sample is pipetted above the fill mark on the transfer pipette and transferred to the sample chamber of the Xpert CT/NG cartridge. The GeneXpert cartridge is loaded onto the GeneXpert Instrument System platform, which performs hands-off, automated sample processing, and real-time PCR for detection of DNA. Summary and detailed test results are obtained in approximately 90 minutes and are displayed in tabular and graphic formats.

Supplies and Reagents

The Xpert CT/NG kit (GXCT/NG-10) contains sufficient reagents to process 10 specimens or quality control samples, and the Xpert CT/NG kit (GXCT/NG-120) contains sufficient reagent to process 120 specimens or quality control samples. 

Storage and Handling • Store the Xpert CT/NG cartridges and reagents at 2 °C – 28 °C until the expiration date provided on the label. • Do not use reagents or cartridges that have passed the expiration date. • Do not open a cartridge until ready to test. Use cartridges within 30 minutes after opening the cartridge lid. • Do not use a cartridge that has leaked

Materials Required but Not Provided

Primary samples must be collected and treated with the appropriate kit: • Xpert CT/NG Vaginal/Endocervical Specimen Collection Kit (CT/NGSWAB-50) or Xpert Vaginal/Endocervical Specimen Collection Kit (SWAB/A-50) or Xpert Swab Specimen Collection Kit (SWAB/G-50) • Xpert CT/NG Urine Specimen Collection Kit (CT/NGURINE-50) or Xpert Urine Specimen Collection Kit (URINE/A-50) • GeneXpert Dx System or GeneXpert Infinity Systems (catalog number varies by configuration): GeneXpert instrument, computer, barcode scanner, and operator manual • For GeneXpert Dx System: GeneXpert Dx software version 4.3 or higher • For GeneXpert Infinity-48 System: Xpertise software version 4.3 or higher • For GeneXpert Infinity-48s or Infinity-80 systems: Xpertise software version 6.0 or higher

Assay/Reagent Handling

Do not substitute Xpert CT/NG reagents with other reagents. • Do not open the Xpert CT/NG cartridge lid except when adding the sample. • Do not use a cartridge that has been dropped or shaken. • Do not place the sample ID label on the cartridge lid or on the barcode label. • Do not use a cartridge that has a damaged reaction tube. • Each single-use Xpert CT/NG cartridge is used to process one test. Do not reuse processed cartridges. • Use of CT positive controls in the NG only assay mode may lead to invalid control results. • Use of NG positive controls in the CT only assay mode may lead to invalid control results. • Do not test the endocervical or patient-collected vaginal specimens received in the laboratory without the swab present. A false negative test result may occur. • CHANGE GLOVES if they come in contact with specimen or appear to be wet, to avoid contaminating other specimens. Change gloves before leaving work area and upon entry into work area. • In the event of a spill of specimens or controls, wear gloves and absorb the spill with paper towels. Then, thoroughly clean the contaminated area with a 1:10 dilution of freshly prepared household chlorine bleach. Final active chlorine concentration should be 0.5% regardless of the household bleach concentration in your country. Allow a minimum of two minutes of contact time. Ensure the work area is dry before using 70% denatured ethanol to remove bleach residue. Allow surface to dry completely before proceeding. Or, follow your institution’s standard procedures for a contamination or spill event. For equipment, follow the manufacturer’s recommendations for decontamination of equipment.

Procedure: 

Important Start the test within 30 minutes of adding the sample to the cartridge

Preparing the Cartridge To add the sample to the Xpert® CT/NG cartridge:

1. Obtain the following items: • Xpert® CT/NG cartridge • Transfer pipette (provided) • Appropriately collected and labeled test sample

2. Open the cartridge lid.

3. Gently invert the transport tube 3 to 4 times to ensure adequate mixing of sample and transport matrix.

4. Unwrap the transfer pipette.

5. Open the transport tube lid, compress the bulb of the transfer pipette, insert the pipette into the transport tube, and release the bulb to fill the transfer pipette above the mark on the pipette shaft (Figure 1). Ensure the pipette is filled with no air bubbles present.

6. Empty the pipette’s content into the sample chamber of the cartridge

7. Close the cartridge.

Turn on the GeneXpert instrument: • If using the GeneXpert Dx instrument, first turn on the instrument and then turn on the computer. The GeneXpert Dx software will launch automatically or may require double-clicking the GeneXpert Dx software shortcut icon on the Windows® desktop. or • If using the GeneXpert Infinity instrument, power up the instrument. The Xpertise software will launch automatically or may require double-clicking the Xpertise software shortcut icon on the Windows desktop.

2. Log on to the GeneXpert Instrument System software using your user name and password. 3. In the GeneXpert System window, click Create Test (GeneXpert Dx) or click Orders and Order Test (Infinity). The Create Test window opens. Figure

3. Create Test Window

4. Scan or type in the Patient ID (optional). If typing the Patient ID, make sure the Patient ID is typed correctly. The Patient ID is shown on the left side of the View Results window and is associated with the test results.

5. Scan or type in the Sample ID. If typing the Sample ID, make sure the Sample ID is typed correctly. The Sample ID is shown on the left side of the View Results window and is associated with the test results.

6. Scan the barcode on the Xpert CT/NG cartridge. Using the barcode information, the software automatically fills the boxes for the following fields: Reagent Lot ID, Cartridge SN, and Expiration Date.

7. The Xpert CT/NG test can be run to detect CT only, NG only, or both CT and NG by selecting Xpert CT, Xpert NG or Xpert CT-NG from the Select Assay menu as shown in Figure 3. From the Select Assay drop-down menu, ensure that the appropriate assay is selected to be run.

8. Click Start Test (GeneXpert Dx) or Submit (Infinity). Type your password in the dialog box that appears. Note If the barcode on the Xpert CT/NG cartridge does not scan, then repeat the test with a new cartridge. Note Only the test result for the assay selected at this step will be collected once the test is started. Both the CT and NG results willl only be collected if the Xpert CT-NG option is chosen. 8. Click Start Test (GeneXpert Dx) or Submit (Infinity). Type your password in the dialog box that appears.

9. For the GeneXpert Infinity System, place the cartridge on the conveyor belt. The cartridge will be automatically loaded, the test will run and the used cartridge will be placed into the waste container. or For the GeneXpert Dx Instrument: A. Open the instrument module door with the blinking green light and load the cartridge. B. Close the door. The test starts and the green light stops blinking. When the test is finished, the light turns off. C. Wait until the system releases the door lock before opening the module door and removing the cartridge.

10. Dispose of used cartridges in the appropriate specimen waste containers according to your institution’s standard practices.

Viewing and Printing Results

This section lists the basic steps for viewing and printing results. For more detailed instructions on how to view and print the results, see the GeneXpert Dx System Operator Manual or the GeneXpert Infinity System Operator Manual.

1. Click the View Results icon to view results.

2. Upon completion of the test, click the Report button of the View Results window to view and/or generate a PDF report file.

Interpretation of Results

The results are interpolated by the GeneXpert Instrument System from measured fluorescent signals and embedded calculation algorithms and will be shown in the View Results window. The Xpert CT/NG test provides test results for CT and NG targets, according to the algorithms shown in Table 1

Table 1.

Possible Final Test Results for CT/NG Selected Assay

Result Text CT1 NG2 NG4 SPC SAC

CT DETECTED; NG DETECTED + + + +/- +/-

 CT DETECTED; NG NOT DETECTED + + - +/- +/-

CT DETECTED; NG NOT DETECTED + - + +/- +/- CT NOT DETECTED; NG DETECTED - + + +/- +/-

CT NOT DETECTED; NG NOT DETECTED - - + +/- +/-

CT NOT DETECTED; NG NOT DETECTED - - -++

INVALID - - - - +/-

INVALID - - - +/- -

Table 2.

Xpert CT/NG Results and Interpretations

CT DETECTED; NG DETECTED  CT target and NG target DNA sequences are detected. • PCR amplification of the CT target and the two NG targets give Cts within the valid range and fluorescence endpoints above the minimum setting. • SPC: Not applicable. The SPC is ignored because CT and NG target amplification can compete with this control. • SAC: Not applicable. The SAC is ignored because CT and NG target amplification can compete with this control. • PCC: PASS; all probe check results pass.

CT NOT DETECTED; NG DETECTED CT target DNA sequence is not detected; NG target DNA sequences are detected. • CT is absent or below the assay detection level; PCR amplification of the two NG targets give Cts within the valid range and fluorescence endpoints above the minimum setting. • SPC: Not applicable. The SPC is ignored because CT and NG target amplification can compete with this control. • SAC: Not applicable. The SAC is ignored because CT and NG target amplification can compete with this control. • PCC: PASS; all probe check results pass.

Reference Range/Expected Values

Not detected

The prevalence of infection with CT and/or NG in patient populations depend on risk factors such as age, gender, the presence or absence of symptoms, the type of clinic, and the sensitivity of the test used to detect infections. During the clinical evaluation of Xpert CT/NG for urogenital specimens, the observed CT prevalence rates in females were 5.3% and 5.4% for vaginal and endocervical swab specimens, respectively; the observed CT prevalence rates were 5.6% and 5.7% for female and male urine specimens, respectively . The observed NG prevalence rates in females were 1.4% for both vaginal and endocervical swab specimens; the observed NG prevalence rates were 1.4% and 3.5% for female and male urine specimens, respectively . During the clinical evaluation of Xpert CT/NG for extragenital specimens, the observed CT prevalence rates were 1.9% for pharyngeal swab specimens and 9.0% for rectal swab specimens, respectively . The observed NG prevalence rates were 8.0% for pharyngeal swab specimens and 8.1% for rectal swab specimens, respectively.

Quality Control

Summary. Each Xpert cartridge produces a valid (positive or negative) test result, an ERROR result, or an INVALID result, depending on performance characteristics of the above internal controls that are run on every cartridge.

Cepheid’s GeneXpert System is a closed platform that employs single-use, self-contained Xpert cartridges. Each Xpert cartridge contains all necessary reagents for the detection of target nucleic acids using the polymerase chain reaction (PCR). As each individual test is performed, the Instrument Status, Sample Processing, Integrity of PCR Reagents, and PCR Efficiency are evaluated. These internal quality control features verify multiple aspects of assay performance for every sample tested.

1. Instrument System Control (Check Status): Once an Xpert cartridge has been loaded into a GeneXpert module and before the sample processing steps begin, the software checks the optics, the readiness of the module’s mechanical components, the ambient temperature of the module to assure proper performance of PCR, and the physical integrity of the cartridge. • If Check Status fails for any reason, the assay is terminated and an ERROR is reported

2. Reagent Control (Probe Check): Probe Check is performed on every cartridge after onboard sample preparation, reagent mixing, probe integrity, and reaction tube filling, but before initiation of PCR. During Probe Check, fluorescence readings are measured in the reaction tube for each probe and compared to default settings established by Cepheid. • If the readings match the default settings, the Probe Check control passes • If the readings do not match the default settings, the assay is terminated and an ERROR is reported

3. Sample Processing Control (SPC)/Cepheid Internal Control (CIC): The SPC and CIC are exogenous (non-sample, non-analyte) nucleic acid pre-loaded in the cartridge that coextracts and co-amplifies along with the sample nucleic acids. The SPC and/or CIC verifies the (i) effectiveness of on board sample processing, (ii) integrity of extracted nucleic acids, (iii) favorable reaction conditions for PCR performance, and (iv) absence of excess PCR inhibitors. • If the SPC or CIC Ct is not within the valid range and the endpoint is below the minimum setting in an analyte-negative test, an INVALID result is reported Genotyping assays do not include an SPC because the presence of at least one target allele indicates that sample processing and PCR reaction conditions were favorable. • If no target allele is detected in a genotyping assay, an INVALID result is reported

4. Internal Quantitative Standard High and Low (IQS-H and IQS-L): IQS-H and IQS-L are two Armored RNA® constructs in the form of a dry bead that goes through the whole assay process. They are used for quantification by using lot specific parameters for the calculation of assay specific RNA concentration in the sample. Additionally IQS-H and IQS-L detect specimen associated inhibition of the RT-PCR reaction.

5. Sample Volume Adequacy (SVA): Ensures the sample was correctly added to the cartridge. The SVA verifies that the correct in-volume of sample has been added in the sample chamber. The SVA verifies the sample addition. • If there is no sample or not enough sample added, an ERROR will be displayed.

6. Sample Adequacy Control (SAC): The SAC is employed in assays that require that the sample contains sufficient patient cells for reliable assay performance. The SAC reagents amplify and detect an endogenous single-copy human gene in the patient sample. The SAC coextracts and co-amplifies with the other nucleic acids in the sample. • If the SAC is not within the valid range and the endpoint is below the minimum setting in an analyte-negative test, an INVALID result is reported

7. Other Control Features (all assays): Cepheid’s Xpert assay software employs proprietary relational algorithms for each amplified analyte. These can include minimum and maximum PCR cycle cutoffs, baseline correction, and additional processes to reduce the effects of unusual curves or target relationships in multiple-target assays. • If the criteria of these algorithms are not met, an ERROR or INVALID result is reported

External Controls: not available in the kit, but they can be used (positive and negative controls).

Calibration

1. Place the Xpert Calibration Software CD 1 in the computer connected to the GeneXpert Dx instrument, or in the kiosk computer for the Infinity.

2. On the computer desktop, right-click the Computer icon and a drop-down menu will appear. Click Open, then right-click on the applicable drive letter for your CD drive. Select Open from the drop-down menu, and the files located on the CD will then be displayed. Find and right-click the XpertCalibration.exe application, and when the drop-down menu appears, click Open to launch the software. Note: The software may take some time to load from the CD.

3. The Terms of Service screen appears. Use the scroll bar to read through the entire document. You will be asked click the check box (below the screen) to verify that you have read and agree to the Terms of Service before continuing.

4. After agreeing to the Terms of Service, the Login screen will appear. Log in with your GeneXpert Dx or Infinity designated USER NAME and PASSWORD (previously assigned to you by your system administrator). After entering your login information, click the forward arrow button at the bottom of the screen to advance to the next screen (the Xpert Home screen). Note: The user name and password are the same ones you used for the GeneXpert Dx or Xpertise software.  

5. If a login error occurs, recheck the USER NAME and PASSWORD entries for errors. If necessary, reenter the information and retry. After entering your login information, click the forward arrow button at the bottom of the screen to advance to the next screen (the Xpert Home screen).

6. Obtain a sufficient number of cartridges for the number of module to be tested. Important: Do not open cartridge packages until you are ready to scan the cartridge barcodes (in step 15). Note: Only an Administrator can exclude (deselect) individual modules from this calibration test. When determining the number of cartridges that will be needed for this test, the user should be aware of the number of modules that they will be calibrating

Click the Collect Calibration Data icon on the Home screen (See Figure 4). After a few seconds, the first Contact Information screen will appear.

8. When the first of two Contact Information screens appear fill out the fields in the two screens. Use the large navigation arrows at the bottom of the screens to move between the two screens. Note that fields marked with “*“are mandatory fields

Note: The ASP-provided ID code for the Service Provider on the Contact Information screen consists of four characters. (As examples for the United States, use US, followed by two digits, such as US01, US28, etc.).

9. When all information has been entered, click the forward arrow button at the bottom of page 2 of the Contact Information screen. The Open Module Doors screen will appear. See Figure 7. Manually open all module doors to enable cartridge loading.

10. After opening all the module doors, click the forward arrow button at the bottom of the screen. The Module Preparation screen will appear briefly, showing the message, “Please, wait. Modules are being prepared.” Important: Note that the Module Preparation screen may appear only briefly, with its length of visibility determined by the number of modules being calibrated. The next screen you see will be the Select Modules screen.

11. Follow the on-screen software instructions. By default, all detected modules will be marked as selected for calibration. Note: A Basic User cannot deselect modules to exclude them from this calibration test. Only an Admin can click on individual modules to exclude them from calibration, if required. For excluded modules (not selected for calibration), the door position (open or closed) does not matter. Two screens are displayed. The screen on the left shows the screen an Administrator would see in which individual modules can be deselected from calibration. The screen on the right shows the screen a Basic User would see where no deselection can be done. To move to the next screen, click the arrow at the bottom of the screen.

Important: GX-XVI and Infinity systems only: When selecting modules on screen, note which module lights are blinking on the system as you select each bank.

12. After selecting the modules, click the arrow button at the bottom of the screen. If you are logged on as an Administrator, the Confirm module selection screen appears. If you are logged on as a Basic User, this screen will not appear (Skip to step 13).

13. If all modules have been excluded in the above step by mistake, a screen will appear, advising you to start over by returning to the Home screen or exiting the program

14. After confirming your module selection, you will advance to the Scan cartridge screen, where you will be prompted to scan the barcode on the Xpert Calibration cartridge.

Note: Verify you have enough cartridges on hand to perform the calibration procedure for the desired number of modules.

15. Remove the test kit cartridge from the package for the module you’ve previously selected, opening only one cartridge at a time.

16. Scan the cartridge barcode. Do not substitute a cartridge with another after it’s been scanned. Note: If the barcode cannot be scanned, skip the cartridge and contact your ASP for a replacement cartridge, if necessary. If the barcode scanner is damaged, missing or incorrectly configured, contact your ASP for guidance.

a. After scanning the barcode of the cartridge, ensure you open (vent) the cartridge lid and then close it for each cartridge as directed by the software in step b through step e below. Important: Do Not add a sample or reagent to the cartridge. Use ONLY the cartridges in the calibration kit provided. Note: After a cartridge barcode is scanned a green light will blink on the system above the module door where the cartridge will be loaded. Note: If, for some reason, you want to skip the cartridge just scanned, click the SKIP button at the bottom of the screen. An overlay will appear asking for confirmation on skipping the cartridge. To SKIP the cartridge, click the forward arrow at the bottom of the screen. To proceed without skipping the cartridge, click the “X” icon at the left bottom corner of the screen. You are urged to rescan a cartridge (or substitute a new cartridge if necessary) to ensure a module is not skipped.

b. Venting the cartridge for two seconds is sufficient. This screen is animated, showing the cartridge lid being opened and closed. After venting, click the forward arrow at the bottom of the screen to continue.

c. Close the cartridge lid and ensure the module door is fully opened to receive the cartridge.

d. Load the cartridge into the module (with the cartridge reaction tube facing away from you), as directed by the software screens.

Note: Be sure to load scanned cartridges in sequence in the next available module. This will avoid loading cartridges in the wrong location or leaving modules empty

e. If you are calibrating additional modules, continue by scanning the next cartridge. Place each individual scanned cartridge into the next selected open module, pressing the module door securely closed until it latches. As each module door is closed and latched, data collection will automatically start on that specific module. The blinking green light above the module will then become steady green, indicating that calibration testing has started. Important: If a module door is not closed completely (until it latches) after loading a cartridge, the screen will continue to display a message to insert a cartridge, and the calibration test will not run. If you are unable to close and latch a module door after several tries, press the skip button at the bottom of the screen to skip the module with the faulty door and move ahead. Notify your ASP so the module can be serviced.

17. Calibration will take approximately 20 minutes to complete after the final module has been loaded for testing. When the calibration test begins, the Data collection in progress screen appears.

Important: If necessary, a retest of a previously run module may be started without waiting for the present module to complete its test, as described in steps 18b through 18d.

18. After test completion, the module door will open and the light above the module will turn off. Press the right arrow to continue. When the test is complete, click the forward button at the bottom of the screen to begin uploading calibration test results to the Xpert Connectivity Center.

For all users: If the test was unsuccessful, the screen shown in Figure 19 will appear, showing module status. A test retry must be performed. Click the Retry icon in the lower left-hand corner of the screen.

If the arrow at the bottom of the screen is pressed when there is an unsuccessful module test displayed the Confirm continue screen will appear.

You have the option of continuing by pressing the right arrow on the Confirm continue Screen overlay. Choosing this option will result in the flagged module not being retested, and you will begin uploading calibration data as described in step 19. Another option is to return to the Press retry or continue Screen to Retry (retest) the flagged module by clicking on the red “X” icon at the bottom left of the Confirm continue screen. The Retry procedure is described in step d which follows.

d. If the Retry icon appears, click the Retry icon and you will return to the Scan Barcode screen to complete the retest on the affected module(s). Note that the retest can be of two possible types:

I Retry with the same cartridge: For example, a message may appear telling you to vent the cartridge, rescan it, and put it back in the module.

II Retry with a new cartridge: If the cartridge was defective, or had already been used, you will be asked to replace it by scanning the barcode on a new cartridge, venting it, and loading it into the module.

Note: During the course of running retests, modules may need to be skipped if the user runs out of Xpert Calibration cartridges. Please contact your ASP for additional Xpert Calibration cartridges. Rerun Xpert Calibration on any modules that were skipped. At the completion of the Xpert Calibration data collection process modules determined to require service will be flagged as locked to further use. Please contact your local ASP for further assistance in replacing modules requiring service.

19. After successful test completion and calibration data collection, click the forward arrow.   if you have an active internet connection. However, if you have never been internet connected, or have lost your functioning internet connection sometime during the calibration test, a Download activation code error screen will appear instead, instructing you to write calibration data to data CD2 to send to your ASP. In this case, continue to step d (under step 25) of this procedure to continue as a user without an internet connection.

Note: With a functioning internet connection, the system should proceed normally (with step 20), and the activation certificate should begin downloading.

20. When the calibration data has finished uploading, a Quality Assurance check will be performed on the data. If the check is acceptable, the activation code certificate will automatically download. If the test is not acceptable, the affected module(s) will require service and will be locked to further use. Please contact Cepheid or your local ASP for further assistance.

21. After the Activation Code Certificate has downloaded, the Activation Code will be applied to each successfully tested module, and those modules will then be identified with a “+” symbol

22. After all the activation codes have been applied to the successfully-tested modules (those green modules which appear with the plus symbols applied), the Activation complete screen will appear. This screen shows the location of the Calibration Data report, which is available for review, if desired.

23. Remove and discard all calibration cartridges. Do not save partial kits (all unused cartridges must be discarded). When complete, click the Exit icon at the bottom of the screen to exit the program.

24. Note that in certain situations, a screen may appear, asking for exit confirmation.

Key Points: 

 Limitations

The Xpert CT/NG test has been validated with the following specimen types, collected with the Cepheid Xpert CT/NG Vaginal/Endocervical Specimen Collection Kit and Xpert Vaginal/Endocervical Collection Kit: • Endocervical swabs • Patient-collected vaginal swabs • The Xpert CT/NG test has been validated with the following specimen types, collected with the Xpert Swab Specimen Collection Kit, Xpert CT/NG Urine Specimen Collection Kit or Xpert Urine Specimen Collection Kit. • Endocervical swabs • Patient-collected vaginal swabs • Male and female pharyngeal swabs • Male and female rectal swabs • Male and female urine • Erroneous test results might occur from improper specimen collection, technical error, sample mix-up, or because the number of organisms are below the limit of detection of the test. • Careful compliance with the instructions in this insert and to the Swab and Urine Collection Kit instruction documents are necessary to avoid erroneous results. • False negative results may occur if the organism(s) is present at levels below the analytical limit of detection. • The Xpert CT/NG test has been validated using the procedures provided in this package insert only. Modification to these procedures may alter the performance of the test. • Because the detection of CT and NG is dependent on the DNA present in the sample, reliable results are dependent on proper sample collection, handling and storage. • With endocervical and patient-collected vaginal specimens, assay interference may be observed in the presence of: blood (>1% v/v) or mucin (>0.8% w/v). • With urine specimens, assay interference may be observed in the presence of: blood (>0.3% v/v), mucin (>0.2% w/v), bilirubin (>0.2 mg/mL), or Vagisil feminine powder (>0.2% w/v). • Collection and testing of urine specimens with the Xpert CT/NG test is not intended to replace cervical exams and endocervical sampling for diagnosis of urogenital infection. Other genitourinary tract infections can be caused by other infectious agents.

Methodology

Real time Polymerase Chain reaction (PCR) performed on the Cepheid GeneXpert platform

 

Maintenance

Daily Maintenance: ‒ Discard used cartridges ‒ Put the dust cover when the system is not in use to limitate dust.

• Weekly Maintenance: - Clean the cartridge bay interior ‒ Restart the system (GeneXpert and Computer)

• Monthly Maintenance: ‒ Clean the syringe plunger rod ‒ Clean the instrument surfaces ‒ Clean the fan filters with soapy water (only for GX with white cover) ‒ Archive the results and save it on external support

Clean surfaces;  

Waived Testing Performed outside the Clinical Laboratory

Effective Date: 
Tue, 06/01/2021
Reviewed: 
Wed, 08/04/2021
Policy: 

On occasion, there may be instances when waived testing may be performed outside the clinical laboratory under the guidance of the Student Health Services Laboratory.  In those instances, the following must be adhered to;

Procedure: 

Permission from the Laboratory Director

Permission from the Laboratory director must be granted for any person(s) to perform any testing outside the clinical laboratory.

Training

Any person(s) performing waived testing must be trained by a member of the laboratory staff.
All training documentation will be kept by the Laboratory Supervisor for a minimum of 3 years
No person(s) may perform any clinical testing without appropriate training documentation

Testing and Quality Control

All person(s) performing testing must perform the test as per documented procedure for that specific test (See SHS Lab Manual).
All person(s) performing testing must perform quality control as per documented procedure for that specific test (See SHS Lab Manual)..

Reporting Results

All results must be reported in a timely manner.
All abnormal results must be documented and reported to Student Health Services in a timely manner.

Patient Population

All testing may only be performed on an approved patient population.  Questions regarding approved populations may be directed to the Student Health Center.

Testing Limitations

Student Health Services may rescind the ability to perform testing for any person or department at any time.  Student Health Services will notify person(s) or departments with as much notice as possible.  Once Student Health Services has rescinded testing ability, testing may no longer be performed.

Key Points: 

Off Site Waived Testing

 

Temporary Covid Testing Site

Effective Date: 
Tue, 04/14/2020
Reviewed: 
Fri, 05/01/2020
Revised: 
Mon, 06/14/2021
Policy: 

On March 4th, 2020, Governor Gavin Newsome declared a State of Emergency and a call was sent out to increase laboratory testing capacity for SARS-2 COVID-19. 

EXECUTIVE ORDER N-25-20

WHEREAS on March 4, 2020, I proclaimed a State of Emergency to exist in California as a result of the threat of COVID-19; and

WHEREAS despite sustained efforts, the virus remains a threat, and further efforts to control the spread of the virus to reduce and minimize the risk of infection are needed; and

WHEREAS state and local public health officials may, as they deem necessary in the interest of public health, issue guidance limiting or recommending limitations upon attendance at public assemblies, conferences, or other mass events, which could cause the cancellation of such gatherings through no fault or responsibility of the parties involved, thereby constituting a force majeure; and

WHEREAS the Department of Public Health is maintaining up-to-date guidance relating to COVID-19, available to the public at http://cdph.ca.gov/covid 19; and

WHEREAS the State of California and local governments, in collaboration with the Federal government, continue sustained efforts to minimize the spread and mitigate the effects of COVID-19; and

WHEREAS there is a need to secure numerous facilities to accommodate quarantine, isolation, or medical treatment of individuals testing positive for or exposed to COVID-19…

WHEREAS in the interest of public health and safety, it is necessary to exercise my authority under the Emergency Services Act, specifically Government Code section 8572, to ensure adequate facilities exist to address the impacts of COVID-19; and…

WHEREAS under the provisions of Government Code section 8571, I find that strict compliance with various statutes and regulations specified in this order would prevent, hinder, or delay appropriate actions to prevent and mitigate the effects of the COVID-19 pandemic.

NOW, THEREFORE, I, GAVIN NEWSOM, Governor of the State of California, in accordance with the authority vested in me by the State Constitution and statutes of the State of California, and in particular, Government Code sections 8567,8571 and 8572, do hereby issue the following order to become effective immediately:

IT IS HEREBY ORDERED THAT:

9. The certification and licensure requirements of California Code of Regulations, Title 17, section 1079 and Business and Professions Code section 1206.5 are suspended as to all persons who meet the requirements under the Clinical Laboratory Improvement Amendments of section 353 of the Public Health Service Act for high complexity testing and who are performing analysis of samples to test for SARS COV-2, the virus that causes COVID-19, in any certified public health laboratory or licensed clinical laboratory.

Procedure: 

In answer to the call, the University of California Santa Cruz established and licensed a Temporary COVID-19 testing site (see approval notice below).

Olena Vaske <olena@ucsc.edu>Re: COVID19 temporary testing site at UC Santa CruzCDPH LFS COVID <LFSCOVID@cdph.ca.gov>Tue, Apr 21, 2020 at 7:03 PMTo: Olena Vaske <olena@ucsc.edu>

Cc: CDPH LFS COVID <LFSCOVID@cdph.ca.gov>, Ralph Green <rgreen@ucdavis.edu>, Elizabeth Miller<emiller3@ucsc.edu>

Dear Olena,

UCSC Student Health Center– CDF-00002057, CLIA 05D0687329 has been approved for one temporary testing site.

COVID-19 Temporary testing site:

1. UCSC Molecular Diagnostic Lab, 1156 High Street, Santa Cruz, CA 95064

Please note that laboratories approved to test for SARS-CoV-2 must report all positive, negative, and inconclusive test results for SARS-CoV-2 daily to the local health officer for the jurisdiction where the patient resides, by telephone and through the Electronic Laboratory Reporting system (ELR). Please see the attached brochure for more information.

Thank you for your efforts during this time of emergency.

The Molecular Diagnostic Laboratory department serves the campus of the University of California Santa Cruz, as well as, the surrounding areas as per the request of Santa Cruz County.  Testing quickly outgrew the space the Molecular Diagnostic Laboratory (MDL) occupied and the department was approved to move to 2300 Delaware St., Santa Cruz CA on March 16, 2021.

The Temporary COVID-19 testing laboratory (MDL) will cease operations on or before June 30, 2022 or when the Governor’s order is rescinded, whichever comes first.  Additionally, the MDL may cease operations once the Laboratory Directors deems there is no longer a need for extensive COVID-19 testing. At such time, all policies and procedures will be retired.

Key Points: 

Given the temporary nature of the MDL, all policies and procedures are stored on a special drive that can accessed via the following link;

OSOM® BVBLUE® TEST

Effective Date: 
Thu, 05/27/2021

Policy:

 

Principle

OSOM® TRICHOMONAS RAPID TEST

Effective Date: 
Thu, 05/27/2021

Policy:

Principle

The OSOM® Trichomonas Rapid Test is intended for the qualitative detection of Trichomonas vaginalis (“Trichomonas”) antigens from vaginal swabs or from the saline solution prepared when making wet mounts from vaginal swabs. This test is intended for use in patients with symptoms of vaginosis/vaginitis or suspected exposure to the Trichomonas pathogen.

Temporary SARS2-COVID-19 Molecular Test

Effective Date: 
Fri, 05/15/2020
Reviewed: 
Thu, 05/27/2021
Policy: 

The California Department of Public Health (CDPH) expects that many CLIA-certified laboratories qualified to perform high complexity testing are eligible to test for SARS-CoV-2, the virus that causes COVID-19, or novel coronavirus infection, and is providing the following information to address laboratory concerns. Emergency Use Authorization and COVID-19 Tests

• On February 29, 2020, the Food and Drug Administration (FDA) issued an immediately in effect guidance with policy for diagnostic testing specific to the COVID-19 public health emergency, along with a template for Emergency Use Authorization (EUA) submissions, and followed it with a new guidance on March 16, 2020. The guidelines and template are available on the FDA website: o Guidance for obtaining approval: https://www.fda.gov/media/135659/download. o Template for EUA submissions: https://www.fda.gov/media/135658/download.

• Please note: The State of California is not authorizing California laboratories to develop and perform tests for COVID-19 at this time and currently has not established a process for authorizing such tests. Laboratories seeking authorization for their own tests for COVID-19 should refer to the FDA Guidance linked above and submit an EUA submission to the FDA as directed in that guidance.

• CDPH requests that any laboratory applying for an EUA please copy Laboratory Field Services (LFScovid@cdph.ca.gov) on the email submitting the completed EUA request to the FDA. Disease Reporting

• On March 9, 2020, the list of reportable diseases in Title 17, California Code of Regulations (17 CCR) section 2500 was amended to include COVID-19 and Novel coronavirus infections, and 17 CCR section 2505 was amended to include SARS-CoV-2 and Coronavirus, novel strains, effective immediately.

o Any laboratories approved to test for SARS-CoV-2 must report all positive, negative, and inconclusive test results for SARS-CoV-2 within one hour to the local health officer for the jurisdiction where the patient resides, by telephone and through the Electronic Laboratory Reporting system

Laboratory and Personnel Requirements

• Please note that any California laboratory performing testing under the provisions of the EUA must hold a valid California clinical laboratory license pursuant to Business and Professions Code (BPC) section 1265.

• If a California laboratory sends biological specimens originating in California for SARS-CoV-2 testing to a laboratory outside the state that does not hold California licensure, the California laboratory can apply for approval to add the out-of-state laboratory as a temporary testing site to test for SARS-CoV-2 for the duration of the emergency.

On March 12, 2020, Governor Newsom issued Executive Order N-25-20, which suspends the certification and licensure requirements of California Code of Regulations, Title17, section 1079 and Business and Professions Code section 1206.5 for the duration of the COVID-19 emergency. This order allows all persons who meet the requirements for personnel performing high-complexity testing specified in Title 42, Code of Federal Regulations, Section 493.1489 to test for SARS-CoV-2, the virus that causes COVID-19, in any certified public health laboratory or licensed clinical laboratory for the duration of the emergency.

o The laboratory director is responsible for the competency assessment and documentation of all personnel testing for SARS-CoV-2.

o This order applies to high-complexity testing personnel. It does not alter the qualifications required of a laboratory director, clinical consultant, technical consultant, technical supervisor, and general supervisor or the supervision requirements in current California law.

o The laboratory director must provide the list of testing personnel along with documentation of competency upon request by LFS.

Procedure: 

In response to Governor Newsome’s call for additional testing laboratories, University of California Santa Cruz (UCSC) developed a SARS2-COVID-19 molecular test based on the CDC template with modifications.  Following the guidelines set above, UCSC applied for and received authorization to set up a temporary COVID testing site. 

The temporary COVID testing site is expected to operate for the duration of the emergency order or June 2022, whichever comes first.

The following policies, procedures and protocols apply specifically to the UCSC lab developed test for SARS2-COVID-19, are temporary in nature and will be retired at the end of the emergency order.

BinaxNow COVID-19 ANTIGEN TEST

Effective Date: 
Wed, 03/03/2021
Policy: 

The BinaxNOW COVID-19 Ag Card is a lateral flow immunoassay intended for the qualitative detection of nucleocapsid protein antigen from SARS-CoV-2 in direct anterior nasal (nares) swabs from individuals suspected of COVID-19 by their healthcare provider within the first seven days of symptom onset. Testing is limited to laboratories certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA), 42 U.S.C. §263a, that meet the requirements to perform moderate, high or waived complexity tests. This test is authorized for use at the Point of Care (POC), i.e., in patient care settings operating under a CLIA Certificate of Waiver, Certificate of Compliance, or Certificate of Accreditation. 

Procedure: 

Materials

Materials Provided Test Cards (40): A cardboard, book-shaped hinged test card containing the test strip Extraction Reagent (1): Bottle containing 7.5 mL of extraction reagent Nasal Swabs (40): Sterile swabs for use with BinaxNOW(TM) COVID-19 Ag Card test Positive Control Swab (1) : Non-infectious recombinant SARS-CoV-2 nucleocapsid antigen dried onto a swab Negative Control Swab: The use of a sterile patient swab ensures appropriate negative results are obtained Product Insert (1) Procedure Card (1) Materials Required but not Provided Clock, timer or stopwatch. 

Quality Control

BinaxNOW(TM) COVID-19 Ag Card has built-in procedural controls. For daily quality control, Abbott suggests that you record these controls for each test run. Procedural Controls: A. The pink-to-purple line at the “Control” position is an internal procedural control. If the test flows and the reagents work, this line will always appear. B. The clearing of background color from the result window is a negative background control. The background color in the window should be light pink to white within 15 minutes. Background color should not hinder reading of the test. External Positive and Negative Controls: Good laboratory practice suggests the use of positive and negative controls to ensure that test reagents are working and that the test is correctly performed. BinaxNOW(TM) COVID-19 Ag Card kits contain a Positive Control Swab and Sterile Swabs that can be used as a Negative Control Swab. These swabs will monitor the entire assay. Test these swabs once with each new shipment received and once for each untrained operator. Further controls may be tested in order to conform with local, state and/or federal regulations, accrediting groups, or your lab’s standard Quality Control procedures. If the correct control results are not obtained, do not perform patient tests or report patient results. Contact Technical Support during normal business hours before testing patient specimens.

Procedure

Specimen Collection:

Test specimens immediately after collection for optimal test performance. Inadequate specimen collection or improper sample handling/storage/transport may yield erroneous results. Refer to the CDC Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens from Persons for Coronavirus Disease 2019 (COVID-19) https://www.cdc.gov/coronavirus/2019- nCoV/lab/guidelines-clinical-specimens.html Anterior Nasal (Nares) Swab Only the swab provided in the kit is to be used for nasal swab collection. To collect a nasal swab sample, carefully insert the entire absorbent tip of the swab (usually ½ to ¾ of an inch (1 to 1.5 cm) into the nostril. Firmly sample the nasal wall by rotating the swab in a circular path against the nasal wall 5 times or more for a total of 15 seconds, then slowly remove from the nostril. Using the same swab, repeat sample collection in the other nostril.

Method of Use:

TEST PROCEDURE

Procedure for Patient Specimens Open the test card just prior to use, lay it flat, and perform assay as follows. The test card must be flat when performing testing, do not perform testing with the test card in any other position.

1. Hold Extraction Reagent bottle vertically. Hovering 1/2 inch above the TOP HOLE, slowly add 6 DROPS to the TOP HOLE of the swab well. DO NOT touch the card with the dropper tip while dispensing.

2. Insert sample into BOTTOM HOLE and firmly push upwards so that the swab tip is visible in the TOP HOLE.

3. Rotate (twirl) swab shaft 3 times CLOCKWISE (to the right). Do not remove swab. Page 5 of 14 Note: False negative results can occur if the sample swab is not rotated (twirled) prior to closing the card.

4. Peel off adhesive liner from the right edge of the test card. Close and securely seal the card. Read result in the window 15 minutes after closing the card. In order to ensure proper test performance, it is important to read the result promptly at 15 minutes, and not before. Results should not be read after 30 minutes. Note: False negative results can occur if test results are read before 15 minutes. Note: When reading test results, tilt the card to reduce glare on the result window if necessary. Individuals with color-impaired vision may not be able to adequately interpret test results.

Procedure for BinaxNOW™ Swab Controls:

Open the test card just prior to use, lay it flat, and perform assay as follows.

1. Hold Extraction Reagent bottle vertically Hovering 1/2 inch above the TOP HOLE, slowly add 8 DROPS to the TOP HOLE of the swab well. DO NOT touch the card with the dropper tip while dispensing.

2. Follow Steps 2 – 4 of the Test Procedure for Patient Specimens

Interpretation

Negative: A negative specimen will give a single pink/purple colored Control Line in the top half of the window, indicating a negative result. This Control Line means that the detection part of the test was done correctly, but no COVID-19 antigen was detected.

Positive: A positive specimen will give two pink/purple colored lines. This means that COVID-19 antigen was detected. Specimens with low levels of antigen may give a faint Sample Line. Any visible pink/purple colored line is positive.

Invalid: If no lines are seen, if just the Sample Line is seen, or the Blue Control Line remains blue, the assay is invalid. Invalid tests should be repeated.

 

 

 

Key Points: 

Limitations

• This test detects both viable (live) and non-viable, SARS-CoV, and SARS-CoV-2. Test performance depends on the amount of virus (antigen) in the sample and may or may not correlate with viral culture results performed on the same sample.

• A negative test result may occur if the level of antigen in a sample is below the detection limit of the test.

• The performance of the BinaxNOW™ COVID-19 Ag Card was evaluated using the procedures provided in this product insert only. Modifications to these procedures may alter the performance of the test.

• False negative results may occur if a specimen is improperly collected, transported, or handled.

• False results may occur if specimens are tested past 1 hour of collection. Specimens should be test as quickly as possible after specimen collection.

• False negative results may occur if inadequate extraction buffer is used (e.g., <6 drops)

• False negative results may occur if specimen swabs are not twirled within the test card.

• False negative results may occur if swabs are stored in their paper sheath after specimen collection.

• Positive test results do not rule out co-infections with other pathogens.

• False negative results are more likely after eight days or more of symptoms. • Positive test results do not differentiate between SARS-CoV and SARS-CoV-2.

• Negative test results are not intended to rule in other non-SARS viral or bacterial infections.

• The presence of mupirocin may interfere with the BinaxNOW™ COVID-19 Ag test and may cause false negative results.

• Negative results should be treated as presumptive and confirmation with a molecular assay, if necessary, for patient management, may be performed.

• If the differentiation of specific SARS viruses and strains is needed, additional testing, in consultation with state or local public health departments, is required.

 

CONDITIONS of AUTHORIZATION for LABORATORY and PATIENT CARE SETTINGS

The BinaxNOW™ COVID-19 Ag Card Letter of Authorization, along with the authorized Fact Sheet for Healthcare Providers, the authorized Fact Sheet for Patients, and authorized labeling are available on the FDA website: https://www.fda.gov/medical-devices/coronavirus-disease2019-covid-19-eme.... However, to assist clinical laboratories using the BinaxNOW™ COVID-19 Ag Card, the relevant Conditions of Authorization are listed below:

• Authorized laboratories1 using your product must include with test result reports, all authorized Fact Sheets. Under exigent circumstances, other appropriate methods for disseminating these Fact Sheets may be used, which may include mass media.

• Authorized laboratories using your product must use your product as outlined in the “BinaxNOW™ COVID-19 Ag Card” Instructions for Use. Deviations from the authorized procedures, including the authorized instruments, authorized clinical specimen types, authorized control materials, authorized other ancillary reagents and authorized materials required to use your product are not permitted.

• Authorized laboratories that receive your product must notify the relevant public health authorities of their intent to run your product prior to initiating testing.

• Authorized laboratories using your product must have a process in place for reporting test results to healthcare providers and relevant public health authorities, as appropriate.

• Authorized laboratories will collect information on the performance of your product and report to DMD/OHT7-OIR/OPEQ/CDRH (via email: CDRH-EUAReporting@fda.hhs.gov) and Abbott Diagnostics Scarborough, Inc. (via email: ts.scr@abbott.com, or via phone by contacting Abbott Diagnostics Scarborough, Inc. Technical Service at 1-800-257-9525) any suspected occurrence of false positive or false negative results and significant deviations from the established performance characteristics of your product of which they become aware.

• All operators using your product must be appropriately trained in performing and interpreting the results of your product, use appropriate personal protective equipment when handling this kit, and use your product in accordance with the authorized labeling.

• Abbott Diagnostics Scarborough, Inc., authorized distributors, and authorized laboratories using your product must ensure that any records associated with this EUA are maintained until otherwise notified by FDA. Such records will be made available to FDA for inspection upon request.

 

References

Abbott laboratories, 2020. BinaxNOW Covid-19 Ag Card Product Insert. https://www.fda.gov/media/141570/download

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Dou C, Xie X, Peng Z, Tang H, Jiang Z, Zhong Z, Tang J. 2020. A case presentation for positive SARS-CoV-2 RNA recurrence in a patient with a history of type 2 diabetes that had recovered from severe COVID-19. Diabetes Res Clin Pract 166:108300. https://doi.org/10.1016/j.diabres.2020.108300.

 Tahamtan A, Ardebili A. 2020. Real-time RT-PCR in COVID-19 detection: issues affecting the results. Expert Rev Mol Diagn 20:453–454. https://doi .org/10.1080/14737159.2020.1757437.

Wu Y, Guo C, Tang L, Hong Z, Zhou J, Dong X, Yin H, Xiao Q, Tang Y, Qu X, Kuang L, Fang X, Mishra N, Lu J, Shan H, Jiang G, Huang X. 2020. Prolonged presence of SARS-CoV-2 viral RNA in faecal samples. Lancet Gastroenterol Hepatol 5:434–435. https://doi.org/10.1016/S2468-1253(20)30083-2.

Corcorran MA, Olin S, Rani G, Nasenbeny K, Constantino-Shor C, Holmes C, Quinnan-Hostein L, Solan W, Snoeyenbos Newman G, Roxby AC, Greninger AL, Jerome KR, Neme S, Lynch JB, Dellit TH, Cohen SA. 20 August 2020. Prolonged persistence of PCR-detectable virus during an outbreak of SARS-CoV-2 in an inpatient geriatric psychiatry unit in King County, Washington. Am J Infect Control https://doi.org/10.1016/j.ajic .2020.08.025.

Surkova E, Nikolayevskyy V, Drobniewski F. 2020. False-positive COVID-19 results: hidden problems and costs. Lancet Respir Med 8:1167–1168. https://doi.org/10.1016/S2213-2600(20)30453-7.

Cohen AN, Kessel B, Milgroom MG. 2020. Diagnosing COVID-19 infection: the danger of over-reliance on positive test results. medRxiv 2020.04.26 .20080911. https://www.medrxiv.org/content/10.1101/2020.04.26.20080911v4.

La Scola B, Le Bideau M, Andreani J, Hoang VT, Grimaldier C, Colson P, Gautret P, Raoult D. 2020. Viral RNA load as determined by cell culture as a management tool for discharge of SARS-CoV-2 patients from infectious disease wards. Eur J Clin Microbiol Infect Dis 39:1059–1061. https://doi .org/10.1007/s10096-020-03913-9.

Ramos KJ, Kapnadak SG, Collins BF, Pottinger PS, Wall R, Mays JA, Perchetti GA, Jerome KR, Khot S, Limaye AP, Mathias PC, Greninger A. 2020. Detection of SARS-CoV-2 by bronchoscopy after negative nasopharyngeal testing: stay vigilant for COVID-19. Respir Med Case Rep 30:101120. https://doi.org/10.1016/j.rmcr.2020.101120.

Service RF. 22 May 2020. Coronavirus antigen tests: quick and cheap, but too often wrong? Science https://doi.org/10.1126/science.abc9586.

Guglielmi G. 2020. Fast coronavirus tests: what they can and can’t do. Nature 585:496–498. https://doi.org/10.1038/d41586-020-02661-2.

Mak GC, Cheng PK, Lau SS, Wong KK, Lau C, Lam ET, Chan RC, Tsang DN. 2020. Evaluation of rapid antigen test for detection of SARS-CoV-2 virus. J Clin Virol 129:104500. https://doi.org/10.1016/j.jcv.2020.104500.

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